The Rikudō Sennin's Legacy
by Death's Scorn
Summary: Naruto is tired of being virtually alone and weak in the world. He wants to change the world for the better, but he needs the power to do so. Luckily he finds it through his secret guardian angel, Itachi. Through accidental genetic modification, Naruto comes into the Legacy of the Rikudō Sennin. AU. Naruto/Harem. Rewrite of older story: The Rikudō Sennin's successor.


**Chapter 1: The Start of a Legacy**

"Yo." Human speaking.

 _'I'm tired of this.'_ Human thinking.

 **"What the hell do you want."** Demon/Summon speaking.

 ** _'Damn brat'_** Demon/Summon thinking.

 **Rasengan** Jutsu or location

Disclaimer: I don't own Naruto.

 **Konohagakure, October 10, Late Evening**

* * *

Konohagakure, the village hidden in the trees, is a prosperous hidden village. Today was a special holiday that the people of Konoha have celebrated for the past 6 years. It is the anniversary of the day that the late Yondamie Hokage, Minato Namikaze, defeated the monstrous Kyuubi no Kitsune, a demon of great strength and power. However it was at the cost of his life.

However, amidst the celebration, there was one who never liked this day. His name was Uzumaki Naruto. He hates today because despite it being his birthday, he never does anything that supposed to make the day feel special and all about him. Instead he was a orphan, recently kicked out of the orphanage, whose parents, from what he was told, died during the Kyuubi attack.

To make matters worse, he is treated by the villagers on a daily basis. He is forced to pay much higher prices at stores and restaurants. However he doesn't make money and So is forced many times to eat out of the garbage without being caught. He is often called demon brat and other names by people under their breaths.

Today was just worse than any other day. When he was at the orphanage, during this day, the people there would physically abuse him, ending with him having large bruises on places that clothing could hide. This year was the first time that he was out in the open during his birthday, so he didn't know what to expect. So he ran all the way up to the top of the Hokage monument and hope that none of the villagers would find him.

With the exception of Sarutobi Hiruzen, who is the Sandamie Hokage and was predecessor and replacement after the Yondamie's death, and Teuchi and Ayame of Ramen Ichiraku Stand, Naruto had no one who cared for him. The Hokage provided a place for him to live after he was kicked out of the orphanage; however it was in the Red Light District of Konoha. As for the Raman Stand, they sometimes gave him food for free or on a discount if he put out advertisements throughout the Village.

For the most part he was alone, afraid and too weak to stop prevent anything. The Hokage did put him into the Ninja Academy; however, he knew they only did the very basics and history of Konoha. He was screwed and wasn't going to learn what he wanted in to survive his hard life. He however would always to hide this and would always put on a sting yet goofy like mask of a personality to hide his pain

As he sat there looking over the village from his vantage point, he suddenly heard the sound of feet walking up behind him. He stiffened as he felt afraid of what might happen, a yelling at and some hits thrown. After several moments of nothing happening, he built up the courage to look behind him and was surprised by what he saw.

It was an ANBU, a member of Konoha's special task force that live in secrecy. Each ANBU member is known by the mask they wear, which is the form of an animal. This specific ANBU was Raven, one that he had seen several times before since he was kicked out of the orphanage.

Unknown to Naruto, the ANBU's name was Uchiha Itachi. As the ANBU looked upon the young child, he couldn't help but feel sadness. He knew the boy was treated badly and that it was because . He also knew of the boy's fake personality that he used to hide his suffering. When he was first assigned to watch over the boy, on orders of the Hokage, he saw first-hand of what the boy went through on a daily bases. He had also heard talk about what went on at the orphanage when Naruto was there. Ever since, he had felt compelled to watch over the boy whenever he could, which was mainly when he wasn't on a mission.

So, after months of looking out for him and figuring out what he could do, he finally figured something out, and it came in the form of his best friend, Shisui. After Shisui had lost one of his eyes to Danzō and gave the other to Itachi. His friend then left a suicide note and had himself completely destroyed so nobody could use his body for an investigation. This was all because Sushi chose to get involved with stopping the coup d'état in a peaceful manner.

Shisui told Itachi to protect his eye and the village as his last words. So he decided that the best way of doing that would be to transplant the eye into Naruto. He could never explain why, but every time he was watching Naruto, he always had this feeling that Naruto, would be the best hope for the world. He never had been one to put blind faith on anything, but with the things he has come to have learn recently.

First of all, he figured out who the parents of Naruto were. For one he remembered the name Uzumaki before, and it quickly struck him, he remembered an Uzumaki woman who would commonly meet his mother and we're best friends. After digging up information the only Uzumaki women to have lived in the village were Uzumaki Mito, the wife of the First Hokage, and Uzumaki Kushina, the wife of the Yondamie Hokage. After finding pictures of the woman it only confirmed who his parents were. Naruto had the head shape of Kushina and a similar personality, but he has the sun missed blonde hair and bright blue eyes of his father. Uzumaki Naruto was actually Namikaze Naruto.

Another was what he learned from the Uchiha Stone Tablet that resides in a secret area of the Naka Shrine. With the help of his Mangekyō Sharingan, he was able to decipher part of the tablet, more so than with just a regular Sharingan. What he read was the story of the legendary Rikudō Sennin, and his powerful dōjutsu, the Rinnegan. Researching the story of the Sage, he learned that he sired the ancestors of two clans: his own, The Uchiha Clan, and their rival clan, The Senju. He quickly learned that the Uzumaki clan members were also descendants of same ancestor of the Senju Clan.

As the story goes, the Sage gave the power of his eyes to one son and the power of his body to the other. So, he wondered, what would happen if the two bloodlines were to mix? Would the child be able to develop the Rinnegan or would they just be able to use the abilities of each clan separately. Either way, there was only one way to find out. For the first to happen, the only thing that could do it since Naruto wasn't born of the two clans was to see if maybe if the chakra of the Uzumaki flowing into the eye would force it to become the Rinnegan. The latter option would that when he transplanted the eye, nothing else will happen, just like it did with Hatake Kakashi.

Before he did this he needing Naruto to pass one final test that will decide if he should give the eye to him.

Back at the scene at hand, Naruto stared at the ANBU in _anticipation for several moments._

"What d-do you want ANBU-san?" asked a nervous Naruto.

"I wish to ask you something," started the ANBU. "If I could give you a great power so that you would not feel weak, how would you end up using such power?" He decided to not give any possible answers to choose from. He was to hear Naruto's own word on this matter.

Naruto pondered this question. _'What would I do with such power?'_ and he thought over it for several minutes until he found his answer.

He put on a brave determined look as he stare into the ANBU's miserable eyes through the mask's eye holes as he said, "I would use it to protect the people I hold precious to me until my dying breath!"

Itachi looked at the young boy, as a small smile formed under his mask, "Good answer."

With that, Itachi moved at great speed and ended up behind Naruto and chopped at the back of the boy's neck and he was knocked out.

Itachi picked up the boy's limp body and jumped off into the woods to find a spot where he would not be disturbed.

* * *

 **Cave, About a Mile from Konoha, Midnight**

Itachi had laid Naruto flat on his back and had pulled out a small jar that contained his late friend's eye. After having everything need for the procedure he quickly started the transplant.

The surgery took 20 minutes to be completed. He placed the eye that he took from Naruto, the left eye, and placed it into the jar.

He put the jar into a sealing scroll and walked to the cave wall and rested against it. All there was to do now was to wait and see what would happen.

Deep within the mind of Naruto, behind a large set of iron bars, a figure shrouded by the shadows stirred. Instantly, an eye with an iris the color of blood red and a slotted black pupil shot wide open.

 **"Sharingan!"** a booming demonic voice cried out. In it's anger it had sent a surge of it's potent chakra to the location of the said item. This in turn set off a mixing of all the things needed that would continue a legacy.

As the mixed chakra of Naruto and the demonic chakra made it to the transplanted eye, it began to change its genetic structure. This changed genetic configuration transferred over to the other eye and changed it to now make a matching pair of eyes.

Back with Itachi, with his Sharingan active, he could see the chakra forming around his eyes. He could sense three different chakra signatures being involved with this: the bit of Shisui's chakra from his eye, Naruto's own immense chakra, and a demonic chakra. _'The Kyuubi,' thought Itachi._

This lasted no longer than a minute before all of the chakra activity stopped. With that over he decided that he would wait for the boy to wake up before he sees the fruit of his labor turns up. For now he could use some rest as he closed his eyes to sleep.

Back with the caged creature, it had quickly realized what it had just created. He decided that it would leave this be for now. He will talk with his host soon, and they would have a talk. He would make sure that his father's eyes will not be used wrongly, even if it would cost his own existence to do so. Until then, he will wait and observe.

* * *

 **Cave, 7:00 A.M.**

Itachi awoke to the sound of someone groaning. Opening his eyes quickly to take in his surrounding h quickly recognized where he was and remembered the events of last night. He turned his head to the source of the groaning that woke him up, and saw Naruto who was beginning to stir.

The first thing Naruto felt was pain, mainly in his eyes. It felt like they had been set on fire and all that was left was a smoldering burn. It took a bit but the pain had lessened to a tolerable level. He opened is eyes and instantly knew he was somewhere he didn't know. He was in a cave and could see most of the inside of the cave thanks to light prov8ded by the sun.

As Naruto looked around, his eyes fell onto a shadowed part of the cave as he noticed a figure was standing there. He started to back up as the figure walked out of the shadows towards him until his back laid up against the back of the wall.

As the face of the man came into view, he recognized the ANBU that he had seen at the top of the Hokage Monument. He also remembers the question the ANBU asked, the answer he gave, and that said ANBU had knocked him out. Now it was just the matter of what the ANBU had done to him that made his eyes burn.

The two stayed several feet apart with silence as they looked at each other. _'It worked far better than I thought it would,'_ thought Itachi.

"How are you feeling Naruto-kun?" asked the ANBU.

Naruto looked at him before answering, "My eyes were hurting when I woke up, but now they don't anymore. What did you do to me?"

"I did what said I would Naruto. I said I would give you power and you told me you would use power to protect those who you care for. That was the answer I was looking for and So gave you the power that would allow you to do just that," answered the ANBU.

"Oh… so what cool power do I have," Asked an excited Naruto.

Itachi had a small smile under his mask. Of course Naruto would get excited over something like this. "What I had given you is something that has only been heard of in myths. It is called…The Rinnegan."

Naruto tilted his head in confusion, "What's that?"

"It's a special dōjutsu, or a ninja eye technique, that belonged to the creator of Chakra and Ninjutsu, the Rikudō Sennin," explained Itachi.

"Awesome, so, what does it do?" asked Naruto as his excitement returned.

"I really don't know what it can do. Not much is known about it as it has not been used by someone before. You are most likely the only person to have ever had it since the era of the Sage. More than likely, you will have to discover what it is capable by training to use it."

"Oh. So how do I do that then? I'm only just started the academy and I don't know much about any ninja skills," asked the young boy.

Itachi thought on that for a few moments, "I won't be around all the time to do so, but when I'm able to, I will train you."

Naruto looked up at the ANBU with big wide eyes, "Really you'll train me?" Itachi nodded. "Yes! When do we start, huh! When, When?!" yelled out Naruto as he jumped in place full of excitement.

Itachi smiled as the boy's excitement. He could never explain why, but the boy's personality could always bring at least a small smile to his face. "It early in the morning and I don't have to be doing anything today so we will train until sunset today. First thing first, we need to learn how to hide your dōjutsu so nobody will be able to see it."

Naruto calmed down, "Huh? Why would I need to do that?" he asked.

"Because, a dōjutsu doesn't just give abilities to the user, it also ends up changing the physical look of the user's eyes." Itachi explained as he reached behind his back and pulled out a scroll.

"Really? So my eyes aren't blue right now?" the ANBU nodded as he opened the scroll and place his hand onto the scroll. With a puff of smoke, there was a mirror in his hands as the smoke cleared.

"Here, why don't you take a look for yourself," and Naruto was handed the mirror.

Naruto accepted the mirror and looked into it. He saw completely purple eyes that had circle go from his pupil like ripple as they continued last his eyelids. To be honest, Naruto thought that they looked kind of weird.

"So why would I have to hide it then?" asked Naruto, handing the ANBU the mirror back

He accepted the mirror and sealing it back into the scroll. "Because Naruto, there are people out there who do know of this eye and will do anything to get a hold of it for themselves. They could end up kidnapping you and either experiment on you or brain wash you. Some would even go as far as to kill you and take the out right out of your sockets. So until you are better prepared to fight off these types of people, you need to keep your eyes hidden from as many people as possible. You understand?" Itachi explained.

Naruto nodded.

"Good then let us begin. You do know hoe chakra flows throughout the body. Right?" Naruto nodded so he continued, "Well, there are tenketsu, or nodes, which stem from the chakra pathway system and are where chakra is released from into and out of the body. There is a tenketsu in each eye that allow ordinary ninja the ability to enhance their vision. Dōjutsu users use this to activate their dōjutsu when they push chakra into their eyes. In order to deactivate them, chakra must stop flowing through those tenketsu points and will return the eyes to their normal state. That is what you will be learning, to turn off the flow of Chakra to your eyes. Once you get that down you will practice activating and deactivating the Rinnegan, until you can do so with ease."

Naruto nodded as he looked at him with a determined look.

"The First step is to be able to feel for your chakra system. The best way of doing that is to meditate and try to concentrate on that feeling once you find it," Itachi stated.

Naruto sat down with crossed legs and with his arms in his lap. "You need to be completely relaxed and calm. Ignore everything in the outside world as you look inside you." And with that, Itachi walked over to the cave wall and sat down as he watched.

Itachi knew that this might not work. With the fact that Naruto was only 6 years old, he would have a hard time doing this. Having such a large amount of Chakra doesn't make things easier. A large amount of Chakra is difficult to control. ' _If this doesn't work out, I'll just have to go with a Genjutsu or a seal to give to him.'_

With Naruto, he had calmed down a considerable amount as he ignore everything around him. He solely concentrated on finding his chakra.

For several hours into early afternoon, Naruto had tried several times to accomplish his goal. On his most recent attempt, he had been able to feel something that seemed to be in his eyes. With that accomplished he focused on that feeling and started to will it to stop The Chakra from flowing into his eyes. It had taken an hour until he couldn't fell anything in his eyes before he opened his eyes to look at his new sensei.

"I think I did it sensei?" asked a joyful Naruto.

Itachi stood up from the wall and walked over to the boy. He looked into Naruto eyes and saw that Naruto had indeed been successful in deactivating the Rinnegan.

"That is good Naruto," he started as he then made his way outside the cave and looked at where the sun was positioned. "We still have four hours before sunset. Now you will use this time to activate and deactivate your dōjutsu at a much faster time. You will want to get it down to at least in a matter of seconds but eventually you will want to be able to do so instantly as because in battle, every second counts," explained the Uchiha.

Naruto nodded and he sat back down. Every time he was able to activate or deactivate it, he was able to do it in a shorter time than the last.

Sunset had finally come and Naruto had managed to bring the time down to just 5 seconds. Itachi was impressed with this and was already making plans on what he will be starting with for Naruto's training.

"Good job Naruto-kun. It's now sunset and it is time that I take you home. I must also return home being gone any longer without my family knowing where I've been will cause them to worry," announced the ANBU.

A tired Naruto nodded as he rubbed his eyes. Itachi crouched down and allowed Naruto to climb into his back. Once Naruto was secured, Itachi jumped off back towards Konoha.

* * *

 **Konoha, Naruto's Apartment, 7:00 p.m.**

Itachi jumped through the open window of Naruto's apartment as Naruto jumped off his back.

"Thanks again sensei. When will I be able to see you again?" asked Naruto.

"No problem Naruto-kun. I will be able to see you on Tuesdays, Wednesdays and some Saturdays. You will see me this coming up Saturday. Until then, you need to train activating your dōjutsu and going to the academy," Itachi explained.

"But I don't want to go to the academy. They aren't teaching us any cool ninja stuff. I don't need any of those science, math, and history classes," Naruto whined.

"Ah, but they are important. Fighting isn't just about what skills and jutsu you have. Those classes can help you plan strategies and plan things out. History teaches you about the mistakes of the past, which is important because those who forget the past are doomed to repeat it. Having strength in both mind and body can make you all the more challenging opponent. So I don't want to hear any more complaining. All of the world's greatest ninja may have had very powerful skills, but they also had the site and intelligence to put those skills to the best use."

Naruto absorbed all of that information in as he thought over what his 6 year old mind could make of this information. Basically, academy means smarter, smarter means better fighter, and better fighter means better protection for those I care for.

Naruto looked up at him with a wide grin, "Okay sensei, I understand."

Itachi hoped so, "Well, I'll see you Saturday Naruto. Have a good night," he said as he walked up to the window, ready to jump out.

"Wait!" yelled out Naruto from behind him. Itachi turned around and waited for Naruto to speak.

"Can you tell me who you are? I promise not to tell anyone," asked Naruto in a quiet voice.

Itachi hesitated for a moment before reaching up to his mask and pulling it off before saying, "My name is Itachi Uchiha," and after placing the mask back into his face, he jumped out the window and vanished.

Naruto stared at the spot where Itachi stood. _'Thank you, Itachi-sensei.'_ He walked into his kitchen finding two cups of ramen and heated them up. After he finished eating, he walked toward his bed and with that he laid down and drifted off to sleep, dreaming of all the things he will hope to do in the future.

* * *

 **Uchiha Clan Compound, Itachi's House, 7:30**

Itachi had finally come home after reporting to the Hokage of his botched story of watching over Naruto. He decided it best not to tell the Hokage quite yet as he often felt there was someone in the room hiding that wasn't one of the ANBU that guarded the Hokage. So he will wait for the right time to do it.

As he walked into the house, he saw that the dining room light was on so he guessed his family were currently eating dinner.

As he walked into the dining room, the three currently eating turned toward him. He ardently noticed that there was an extra plate at the table, most likely for If he showed up.

"Hello sochi-kun" called out his mother, Mikoto, with a smile on her face.

"Hey Onee-san!" yelled his younger brother, Sasuke.

His father, Fufaku, just went back to eating barely acknowledging his son with a small nod.

Itachi walked over and sat down on his end of the table, in front of his father, and started to place food onto his plate and started to eat as everyone else continued eating.

Fugaku was the first to finish when he announced, "I'm going to a late night meeting. Mikoto, I will most likely not be back until late at night. There will be no need to wait for me. I wish you all a goodnight."

He soon left the house and the finished eating. As Mikoto cleaned the table, Itachi walked up the stairs towards his room, carrying his gear, with Sasuke quickly running up behind him.

"Hey, Onee-san, are you going to be training tomorrow? If you are can I come watch?" Sasuke called out hoping he would say yes.

Itachi stopped and thought for a moment. "I won't be training tomorrow. I will be busy doing something else. Maybe Friday, Otouto." He said as he poked Sasuke's forehead.

With, that Itachi finished up the stairs and walked into his room, closing the door behind him. He lied down in his bed thinking of what to do for Naruto training for a couple of hours before he succumbs to sleep.

* * *

 **Itachi's Dreamscape**

Itachi awoke to an open area, lighted only by the moon. As he wondered where he was he heard something behind him. He quickly got into a fighting stance as he tensed up, ready to fight who ever it was.

His gaze fell upon a figure who was sitting down. He couldn't see his face as he was bowing his head down and had a large hat made of straw atop his head.

As he was about to speak, when the figure spoke up, his voice identifying the figure as male "You have no need to fear me Uchiha Itachi. I am a friend. Please, sit," the man finished as he place logs into a pile between them and lit the logs on fire with a simple Katon jutsu.

Itachi hesitated a moment before he slowly sat down, warily keeping an eye on the man.

"Who are you?" Itachi said as he fully sat down.

There was silence for several second as the man poked at the fire to keep it going before he spoke, "My name is Ōtsutsuki Hagoromo _."_

Itachi was about to ask if that was supposed to mean something to him but Hagoromo continued, "But you know me better as The Rikudō Sennin," and with that the man looked up to Itachi and looked him straight in the eye and Itachi quickly recognized the Rinnegan in all its glory.

* * *

 **End Chapter One**

 **So what did you guys think of the rewrite. Please leave a review on what you think and if you have any suggestions. Follow and Favorite if you wish. Haters will be ignored.**

 **Now to explain why I had decided to wait so long on making the rewrite is because of two things: 1) I had lost some interest in Naruto fandom as I discovered that I liked other fandoms such as Bleach and Harry Potter more than I did Naruto. 2) I felt that I wanted to wait until the end of the Naruto anime series. Especially since they had added more on the Rikudō Sennin and his past, a key figure of this story.**

 **That leads me to another thing, the complete twist on why I went from a Naruto who hates the village to someone who is neutral to it currently. This is because of the Sage's belief of how peace should be achieved. I felt that a dark hateful Naruto is the opposite of the Sage's and so, I scraped the original story and stated from scratch. Also as a warning, there is a good chance of there being a complete AU by the time Shippuden get here, but that is not a guarantee.**

 **Now as for Itachi. He is going to be a main character of this story. Throughout the story, I hope to include many scenes of what Itachi will go through on his own. The story will focus on Itachi less after the Uchiha Clan Massacre and before the time of Naruto Shippuden starting. Now because Itachi will be playing such a major role, I want to give him someone that he can grow to love. I want you, the readers, to give me some suggestions. I will take the most commonly offered suggestions and make a poll out of it, and there will be no more than three on it. The only rules are that it can't be any of Naruto's girls, and choices that won't be accepted are Sakura, Hinata, Tenten, Karui and Yugao as I already have them paired with someone. Also there will be not yaoi and gender bending allowed.**

 **As for who will be in Naruto's harem here they are: Samui, Konan, Anko, Mei, Kurenai, Ino, Temari and the possibility of one more. It will just depend on how I handle these 7 first and see if she ends up being the one paired with Itachi. The last reason is very unlikely however.**

 **Well I think that's it for the explanation for now.**

 **Again hoped you enjoyed it. I'm already working on the next chapter.**

 **Death's Scorn out.**


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